| Two recombinant inbred line (RIL) populations derived from Zhenshan 97B/Miyang 46 and Xieqingzao B/Miyang 46 (hereafter referred to ZM-RIL and XM-RIL, respectively) and their genetic linkage maps were employed to map the quantitative trait loci (QTL) with main effects, epistasis, and G X E (GE) interaction effects of some important agronomic, grain quality, and anti-abiotic stress traits in different environments or with different treatments. The objective of this study was to understand the genetic basis of these traits more clearly at the molecular level. The main results were as follows.1.Tillering angle: The XM-RIL population and its genetic linkage map were used to map QTLs controlling the tillering angle in two environments,Hangzhou and Hainan. A total of two QTLs with main effects and three pairs of additive X additive double QTL interaction effects were identified. For the main effect QTL, qTA8-2 was detected with LOD of 21.7 and could explain 23.2% of the total phenotypic variations; qTA9-2 was detected with LOD of 22.0 and could explain 19.5% of the total phenotypic variations. The additive effects of the former QTL came from female parent, but latter one came from the male parent. No GE interaction effect was detected for the main effect QTLs. The three pairs of double QTLs interactions only explained 7.69% of the total phenotypic variation, suggesting their minor importance.2. Shattering: The ZM-RIL population and its genetic linkage map were used to map the QTLs controlling the shattering trait in two environments, Hainan and Hangzhou. The results indicated that the shattering of different lines ZM-RIL population varied dramatically in different environments. In Hainan, this triat nearly showed the normal distribution, while in Hangzhou, it showed distorted distribution. A total of eight QTLs with main effects were detected on the chromosome of 1, 2, 3(two QTLs), 6 (two QTLs), 7 and11. Each QTL only contributed little (from 1.7% to 3.9%) to the total phenotypic variations, even in total they only explained 9.05% of the variations. Of them, three QTLs (qSH3-l, qSH3-2 and qSH6-l)had significant GE interaction effects, and their effects increased shattering in Hainan and decreased it in Hangzhou. The total contribution ofthese GE interaction QTLs were as large as those QTLs with main effects, suggesting that GE effects were important for shattering. In addition, five pairs of epistasis QTLs were detected with each contributing to 0.47%-0.85% of the total variation, even in whole, they only explained 3.39% of the total variation. No epistasis by environment interaction effect was detected in this experiement.3. Stigma extruding: The XM-RIL population and its genetic linkage map were used to map QTLs controlling the stigma extruding trait in two environments, Hainan and Hangzhou. The stigma extruding rate was higher in Hainan (21.83%) than that in Hangzhou (8.35%) . Only one QTL with main effect was detected with LOD as high as 28.16, which explained 14.14% of the total phenotypic variations. The positive additive effect of this QTL was 5.10% which came from the female parent. No GE interaction effect was detected. Three additive X additive double QTL epistasis effects were detected with little contributions, and no epistasis by environment effects was detected.4. Rice grain transparency. The ZM-RIL population and its genetic linkage map were used to map QTLs controlling rice grain transparency which was indexed as ratio of light permeating the milled rice grains in two environments. A total of five QTLs with main effects were detected on chromosomes 2, 6 (two QTLs), 8 and 10, which in total contributed to 19.15% of the total phenotypic variations. Among them, the additive effects of qTR2-2 came from the female parents while the others four (qTR6-1 qTR6-2 qTR8-2>qTR10) came from the male parent. The QTL qTR6-l was also detected significant GE interaction effects. In addition, two pairs of additive X additive epistasis QTLs were detected, but they did not show GE interaction effect.
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